Reference SNP(refSNP) Cluster Report: rs12562659

Reference SNP(refSNP) Cluster Report: rs12562659

refSNP ID: rs12562659
Organism:	human (Homo sapiens)
Molecule Type:	Genomic
Created/Updated in build:	120/129
Map to Genome Build:	36.3

Allele
Variation Class:	SNP: single nucleotide polymorphism
RefSNP Alleles:	A/G
Ancestral Allele:	G
Clinical Association:	unknown

HGVS Names
NM_182663.2:c.580-21694G>A
NM_182664.2:c.580-21694G>A
NM_182665.2:c.120+3886G>A
NT_021877.18:g.252686G>A

Links

SNP Details are organized in the following sections:

Submitter records for this RefSNP Cluster

The submission ss19834860 has the longest flanking sequence of all cluster members and was used to instantiate sequence for rs12562659 during BLAST analysis for the current build.

NCBI Assay ID	Handle\|Submitter ID	Validation Status	ss to rs Orientation /Strand	Alleles	5' Near Seq 30 bp	3' Near Seq 30 bp	Entry Date	Update Date	Build Added	Molecule Type	Freq Warning	Ancestral Allele	Success Rate
ss19834860	CSHL-HAPMAP\|CSHL-HuFF-200402.chr1.NT_021877.16_198014		fwd/T	A/G	gttaatagataaacctctatcttcccactg	agactcctcctcatgtgtgtttttctctgt	02/21/04	03/04/04	120	Genomic			unknown
ss20518165	SSAHASNP\|WGSA-200403-chr1.chr1.NT_021877.16_198014		fwd/T	A/G	gttaatagataaacctctatcttcccactg	agactcctcctcatgtgtgtttttctctgt	03/18/04	03/18/04	123	Genomic			unknown

Fasta sequence (Legend)

 ACTTCAGGCT GGGTCAGGTT TTGAAAGGTC CTTCCCATCC CTCCATTCCT TAAGGCATGC
 TAGCTAAGGG GACATTGACC CTACACTTGA TTTTAGCAGG TAGTCCCTGT AATCTTACAA
 CTTTAGTGAC TTAAAAGTTC TTCTTGGTGT CTATCCTACA ACTGAAATAT GTTAATAGAT
 AAACCTCTAT CTTCCCACTG
 R
 AGACTCCTCC TCATGTGTGT TTTTCTCTGT GGATACAAAG AACAGAAGGT TGACTATATC
 TACAGTTAAA TATttttctt tttctttttt tttttttttt tttgagatgg agttttgctc
 ttgttgccca ggctggagta caatgacgcg atctcggctc actgcaacct ctgcctccca
 ggttcaagca attctcctgc ctcagcctcc tgagtagctg agattacagg cacccaccac
 cacacccagc taagttttgt gttttttttt ttgagtagag acagggtttc acaatgttgg
 ccaggtcttg aactcctgac ctcaggtgaa cccctacctc ggcctcccaa ggtgctggga
 ttacaggagt gagccaccgc acccggccTA TAGTTAAATA TTATACTTAA GTACATAGAA
 AACACACTCC CATGCCCCCA TCTGCCTAGG CTTTCTTGGG TCTACAGTGA CACCATTGAA
 TTCTTTTTCT TCAAGGAAGA

GeneView

GeneView via analysis of contig annotation: RASSF5 Ras association (RalGDS/AF-6) domain family member 5

View variations for gene:

Include clinically associated:

in gene region cSNP has frequency double hit

Group
Label

Contig->mRNA

Gene Model (contig mRNA transcript) Color Legend

reference

NT_021877->NM_182663

function

reference

NT_021877->NM_182664

function

reference

NT_021877->NM_182665

function

HuRef

NW_001838536->NM_182663

function

HuRef

NW_001838536->NM_182664

function

HuRef

NW_001838536->NM_182665

function

Celera

NW_926794->NM_182663

function

Celera

NW_926794->NM_182664

function

Celera

NW_926794->NM_182665

function

Group label	Contig-->mRNA-->Protein	Contig position	mRNA orientation	Function


reference	NT_021877->NM_182663->NP_872604	252686	forward	intron

reference	NT_021877->NM_182664->NP_872605	252686	forward	intron

reference	NT_021877->NM_182665->NP_872606	252686	forward	intron

HuRef	NW_001838536->NM_182663->NP_872604	166030	forward	intron

HuRef	NW_001838536->NM_182664->NP_872605	166030	forward	intron

HuRef	NW_001838536->NM_182665->NP_872606	166030	forward	intron

Celera	NW_926794->NM_182663->NP_872604	152113	forward	intron

Celera	NW_926794->NM_182664->NP_872605	152113	forward	intron

Celera	NW_926794->NM_182665->NP_872606	152113	forward	intron

GeneView: no link established by BLAST analysis of mRNA sequences

Integrated Maps:

NCBI MapViewer: rs12562659 maps exactly once on NCBI human chromosome 1

Chromosome	Contig accession	Contig position	Chromosome position	Hit orientation	Contig Allele	Assembly Type	Group label	Contig label	Neighbor SNP	SNP_flank position
1	NW_001838536.1	166030	177433226	plus	G	alt_assembly_8	HuRef	HuRef	view	200
1	NW_926794.1	152113	179986353	plus	A	alt_assembly_1	Celera	Celera	view	200
1	NT_021877.18	252686	204801530	plus	G	ref_assembly	reference	reference	view	200

NCBI Resource Links

Submitter-Referenced
GenBank
NT_021877

dbSNP Blast Analysis
GenBank HTGS Finished:
AL354681.8 NC_000001.9

Population Diversity

There is no frequency data.

Validation Summary:

Validation status	Marker displays Mendelian segregation	PCR results confirmed in multiple reactions	Homozygotes detected in individual genotype data
	UNKNOWN	UNKNOWN	UNKNOWN

Disclaimer Privacy statement

Revised: May 25, 2006 1:38 PM .